


Betrayal

by Duffydog



Category: Star Trek: Voyager
Genre: Episode Related, F/M
Language: English
Status: Completed
Published: 2019-10-20
Updated: 2019-10-20
Packaged: 2020-12-24 12:41:11
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 4,718
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/21099629
Author URL: https://archiveofourown.org/users/Duffydog/pseuds/Duffydog
Summary: I’ve often thought that Chakotay was remarkably tolerant of Janeway’s and Tuvok’s actions in shutting him out of the command structure while they searched for Seska’s spy aboard Voyager. This story explains how he might not have been as tolerant as he appeared.





	Betrayal

**Author's Note:**

> Disclaimer: As usual, characters belong to Paramount, as well as specific dialogue from “Investigations.”
> 
> Many thanks to Brianna Thomas and Shayenne for analysis and helpful comments.

Commander Chakotay stared slack-jawed at Captain Janeway. “Are you saying Paris’ insulting behaviour – the gambling, being late for duty, mouthing off at me – was all a ruse?”

In an obvious attempt to deflect criticism away from his captain, Lieutenant Tuvok cut in smoothly. “That is correct. It was important that his reason to leave the ship appear plausible, so he began behaving like a malcontent.”

The commander’s mouth snapped shut as anger began to flare. Through gritted teeth, he all but snarled. “And the reason I wasn’t let in on this little plan?”

Tuvok’s voice never changed – he might have been explaining Neelix’s menu. “I was the one who recommended to Captain Janeway that you not be told. I suspected the spy was a Maquis and felt it was wrong to put you in a position of setting a trap for someone who had once served under you.”

As an excuse, it was pretty sad, and Chakotay saw through it at once. “In other words, you didn’t trust me.”

Much as she appreciated Tuvok’s efforts, the captain could see he was only exacerbating an already difficult situation. “Commander,” she interrupted with a disarming smile, “the simple fact is we needed a good performance. I’m afraid we used you….”

* * *

Captain Janeway’s words rang over and over in Chakotay’s head as he strode agitatedly to his quarters.

_A good performance,_ he thought to himself, recalling the captain’s excuse. _What about the performance I put on for Seska’s benefit when we tried to find out who had given technology to the Kazon? It seemed my ‘performance’ was good enough then, despite the fact I was aware of the trap we were setting. How was this situation any different? In fact, it would have been easier this time since I didn’t have to deceive someone who knew me very well. The real truth is Janeway doesn’t trust me and never has, despite her protestations to the contrary._ He heaved a great sigh. _So what do I do now?_

His footsteps slowed as he approached his door; a quick press of his fingers on the control panel and it slid open. He stepped through, hearing the door hiss shut, and slumped in relief. In the privacy of his cabin, he could let go of the façade, the pretense that everything was all right, that the command team remained united, when in fact, it wasn’t united at all. Janeway and Tuvok were the de facto command team and he the odd man out.

Wordlessly, he snarled in anger and frustration, kicking off his boots and letting them lie where they fell. Pacing to the viewport, he gazed out at the unfamiliar stars streaking by at warp, feeling more alone than he had in years, since his first day as a new cadet at the Academy. As his fingers drummed idly on the sill, he contemplated his options. He could stand here and continue to feel sorry for himself, he could work on next week’s duty roster, or…he could go on a vision quest, which might help to calm his mind, if his animal guide was feeling cooperative; lately, she had been more capricious than usual.

Fetching his medicine bundle, he sat cross-legged on the floor and began the familiar ritual, hoping for some guidance or at least a little advice. But at the end of half an hour, he was more frustrated than ever. Despite repeated attempts, his animal guide was nowhere to be found. Why she had deserted him, he didn’t know – she simply wasn’t there.

Words rolled softly from his mouth, ancient words of prayer and entreaty, in the old tongue of his people. “Spirits of my ancestors, help me to see my way, tell me what path I should follow. I’m lost and alone, abandoned by all.”

In silence, he waited, but there was no response. Despairing, he dropped his head into his hands, shutting his eyes as he stared down into a black well of desolation. No hope, no anything – he was alone with his misery.

* * *

In the days that followed, after Michael Jonas was exposed as Seska’s spy, and Tom Paris was basking in congratulations from every side on the reality of his deception, Commander Chakotay did his best to carry on as usual and not allow himself to sulk. However, it wasn’t easy.

Once again, the entire crew had been made aware that their first officer, noble and intrepid though he might be, had been the victim of duplicity. And this time not by yet another spy hiding in his crew, but by his captain and fellow officers. In plain words, they’d made him look like a naïve, trusting fool.

Although he tried to hide his feelings behind a stoic facade, resentment and suspicion continued to fester in his soul, colouring his actions as he found himself constantly examining the motives of his crewmates for hidden agendas. The relentless pressure began to tell on his nerves, more than once leading him to snap at some hapless crewman over a minor transgression.

* * *

A week after Tom’s revelations, several of the crew gathered around B’Elanna Torres as she ate a late dinner in the mess hall, begging her to intervene with the commander. Up to now, he’d always been a calm, fair, easygoing man, but in the last week he’d metamorphosed into a harsh taskmaster, his temper unpredictable, meting out punishment for every infraction of the rules, no matter how trivial.

As various tales of woe were related, B’Elanna nodded thoughtfully – she knew Chakotay had been quieter and more withdrawn lately, but in her concern to get the ship repaired as quickly as possible, she hadn’t had time to think about anything else. After all, everyone needed downtime now and then, and not always at the most convenient moment.

However, when yet another tearful ensign quoted the first officer’s stern words earlier that day after she’d handed in a report ten minutes late, B’Elanna had had enough. “Fine!” she exclaimed testily through a mouthful of casserole, “I hear you! I’ll go talk to him.” At the anxious looks from all sides, she added, “Tonight. When I’ve finished dinner.”

There were sighs of relief from her audience, which began to break up as those on shift headed back to work, and the rest departed for various leisure activities.

Left alone, B’Elanna sipped from her cup as she contemplated what she’d heard. It struck her that Chakotay’s suddenly abrasive attitude must be visible to others as well as the individuals directly affected by it, so why were so many complaints about him coming to her? Her own people, she could understand – that would be following the chain of command – but Jenkins for example, worked in one of the science departments; she didn’t have anything to do with Engineering. Hadn’t anyone on the senior staff noticed how unhappy he was? What about the captain, for pete’s sake?! She was supposed to be working closely with him, wasn’t she? Hadn’t she seen anything? Or was everyone on the bridge so busy patting that pig Paris on the back that no one had bothered to pay attention to anyone else?

Sighing, she pushed aside that puzzle to concentrate on the best way to approach her old friend. In normal circumstances, she’d simply march up to him and demand to know what the hell was going on. However, in this case, perhaps that wouldn’t be the best plan of attack. She’d have to be more subtle in her approach, try and sound him out gently in order to get some answers. Finishing her coffee, she rose to her feet and trotted out the door.

“Computer,” she demanded, as she headed towards the turbolift. “What is the location of Commander Chakotay?”

“Commander Chakotay is in his quarters.”

“Is he alone?”

“Affirmative.”

In the peace and solitude of his room, Chakotay was attempting yet again to meditate, but his thoughts were too chaotic to achieve the calm necessary to soothe his mind. Frustrated, he finally gave up, got to his feet and began to dictate his personal log, detailing his actions that day and the reasons for them.

Halfway through this exercise, his door chimed.

“Enter.”

Glancing up, he wasn’t surprised to see his oldest friend standing in the open doorway, checking him over carefully with a speculative look in her eye.

“Don’t just stand there, B’Elanna,” he snapped, when she made no move to enter. “Come in.”

Her eyes rolled slightly at his tone of voice, but she stepped forward enough to allow the door to close

“I wanted to make sure it was safe,” she tossed at him cheekily. “From what I’ve been hearing lately, you’re like a bear with a sore head.”

Chakotay made a face but remained silent, watching as she settled into a chair.

“So,” she continued, her tone more serious now, “want to talk about it?”

“About what?” came the guarded reply.

B’Elanna threw up her hands in exasperation – obviously ‘subtle’ wasn’t going to get her anywhere. “Chakotay! Tonight, while trying to eat my much-delayed dinner in peace after spending six hours wrestling with the plasma injectors, I was interrupted three times by seven different crewmembers all complaining about your recent behavior. Jenkins was actually in tears because you tore a strip off her for handing in a report ten minutes late. Now! You tell me! What’s going on?!”

His head was down, eyes focused on his hands clasped in his lap. When he eventually looked up at her to reply, his face was a neutral mask. “There’s nothing ‘going on’, as you phrase it,” he replied evenly. “Obviously, Jenkins and the others are overreacting. It goes to show how lax things have become on this ship when a crewmember complains about a mild reprimand – which was well-deserved, I might add. Until now, I’ve tried to cut them some slack because of our unique situation but I’m beginning to think that was a mistake.”

B’Elanna stared at him in astonishment. “Chakotay, listen to yourself! You sound like the worst kind of Starfleet tyrant! What’s the matter with you?”

His face set into hard lines as he abruptly rose to his feet. “You’re out of line, Lieutenant. Now, unless you have something else to discuss, please leave me alone.”

Her jaw dropped. “You’re pulling rank on me?!”

He remained silent, staring at her implacably.

As she tried to find words to reason with him, the thought flashed through her head that this wasn’t the Chakotay she knew – something very serious must have happened to provoke such a drastic reaction from him. If only she could get him to open up a bit…. Rising to her feet, she searched his face for any sign of relenting, but his mouth remained a grim line as he stared at her coldly. Reluctantly, she turned to the door, looking back as it opened.

“If you want to talk,” she began, but his only response was a shake of the head. A moment later, she was standing in the corridor. Returning slowly to her quarters, she pondered what she might try next in order to reach him, but was unable to think of anything – Chakotay’s behaviour had been so completely atypical that she felt as if, overnight, he’d become a total stranger.

For several minutes, she debated whether to contact Ayala, who had also been close to Chakotay in their Maquis days, but in the end, her weariness caught up with her and she fell into bed, exhausted. She’d talk to Chakotay again in a day or two, she told herself as she fell asleep, maybe he’d just been having a bad day….

* * *

Meanwhile, Chakotay tried in vain to ignore the feelings of guilt over the way he’d treated his old friend. B’Elanna had only been trying to help, he knew, but right now, he was still too angry and confused to explain the reasons for his behaviour. Indeed, as yet, he wasn’t sure he understood them himself. Her statement, however, that the crew was rapidly learning to fear him, was enough to convince him that he couldn’t remain any longer in the position of first officer.

The first thing he’d learned in command school was that a senior officer never took out his bad temper on his subordinates; without exception, it held true in every situation, no matter the extenuating circumstances. He was no longer fit for command and must submit his resignation, the sooner the better.

Sighing heavily, he turned to enter his bedroom and prepare for bed, his heart heavy with the knowledge that the next day wouldn’t be any easier.

* * *

Early the following morning, Chakotay stood motionless on the bridge, waiting for the arrival of Captain Janeway and the start of Alpha shift. Right on schedule, the turbolift doors opened and she stepped out, coffee mug already in hand. Her face took on a slightly wary cast when she spotted him, but she greeted him pleasantly enough before starting to turn towards the ready room door.

“Captain,” he spoke up. “May I speak with you, please?”

“Can it wait until lunch, Commander?” she demurred, waving the coffee. “I have a meeting in half an hour with Tuvok, and I haven’t read his latest security report yet.”

Struggling to keep his voice completely calm, Chakotay picked up a PADD on his chair and moved to intercept her. “I apologize, Captain, but this is an urgent matter. I need to meet with you as soon as possible.”

Janeway peered at him, her face becoming worried at his serious expression. Whatever he had to tell her, she knew she wasn’t going to like it. However, she had no option but to listen. “Very well. Come on in.”

Trailing through the ready room doors behind her, Chakotay came to a halt in front of her desk as she moved behind it to settle into her chair. He reached for his rank bar, pulling it off and placing it together with the PADD on her desk.

“I must inform you, Captain,” he began formally, “that I am resigning my position as first officer of this ship, as well as my field commission, effective immediately.”

Janeway sat frozen in her chair, mug raised halfway to her mouth, eyes staring at him in total shock.

Without another word, he turned on his heel and strode out of her ready room.

Nearly a minute passed before the captain was able to move. Tapping her combadge, she tried to hail him, but there was no response. Scurrying out of the ready room, her eyes quickly scanned the bridge, but one glance was sufficient to tell her he wasn’t there. She stood motionless, unable to think rationally, her mind in turmoil, able only to focus on the fact that he wasn’t where he should be, namely, at her side. She had to find him and fast.

“Tuvok!” She glanced up at the Vulcan. “You have the bridge.”

“Yes, Captain,” came the calm reply.

Trotting into the turbolift, she waited for the doors to close before asking the computer for Chakotay’s location.

“Commander Chakotay is in his quarters.”

Good. “Deck three.”

Moments later, she was standing in front of his door, finger pressed on the chime.

Chakotay’s door slid open to show his quarters in darkness, the only light shining out from the bedroom.

Janeway stepped in hesitantly, looking around at the unfamiliar surroundings. In the year and a half since they’d been thrown into the Delta Quadrant, she had only been here once before, not long after they’d begun their long journey home.

“Chakotay?” she called out, when she didn’t see him.

“I’ll be there in a minute,” came his answer, sounding slightly muffled.

She tried to determine his mood from his tone of voice, but gave it up as a lost cause and moved a little further into the room, careful not to trip over any furniture.

A moment later, Chakotay appeared in the doorway. “Lights!” he commanded, before apologizing. “Sorry, Captain, I was in a hurry; I forgot they weren’t on.”

Again, surprise reduced her to silence. He had changed out of his uniform, and was dressed in the clothes he’d been wearing when he first arrived on her ship.

“Since I’m no longer an officer, I shouldn’t be wearing a uniform,” he murmured in answer to the astonished look on her face.

His words, spoken in such a soft tone, slammed into her with the force of a sledgehammer. He really meant what he’d said in the ready room. Kathryn felt her heart thump hard, enough to galvanize her into speech.

“Chakotay! I don’t understand why you’re doing this! Why are you resigning? What is going on? At the very least, you owe me a damn good explanation.”

His expression completely neutral, Chakotay looked directly into her face. “I would have thought it was quite obvious. A captain must have complete faith in her first officer. Since obviously, you don’t have that faith in me, I cannot properly fulfill my obligations. Therefore, I’ve resigned to allow you to pick someone else who will be better suited to the position.” He paused before adding, “Actually, I would recommend you choose Tuvok, since you’ve amply demonstrated you have complete faith in _him_.”

Kathryn gasped both in shock and burgeoning fury. “Chakotay! You’re wrong! I do – ”

Cutting her off abruptly, he spoke in a flat tone of voice. “Don’t bother denying it; we both know it’s true.”

Again, she opened her mouth to protest, her eyes flashing with rage, and again he waved her to silence, staring at her quite unmoved.

“You chose to undercut me publicly and let the entire crew watch Paris make a fool of me. How can you possibly think they’ll accept my authority now? Just how stupid do you think I am?!” His voice rose on the last sentence as anger got the better of him. “You’ve humiliated me enough, Captain, and I refuse to allow you to do so any longer. Rather than continue as your first officer, I’d prefer to help Neelix in the mess hall. The less I have to do with you, the better.”

Staring at him in horror, Kathryn was momentarily at a loss for words, too stunned by his string of accusations to rebut them. Starfleet captains, however, are trained to think on their feet and Kathryn was one of the best. Gathering her authority around her like a cloak, she straightened her spine and prepared to go on the attack.

“You have no right….” She began only to have him interrupt her.

“I have every right.” His belligerent tone abruptly became less confrontational, as he fought down his emotions. “When a captain can no longer trust an officer serving under her, she has no choice but to remove that officer from the chain of command. That’s a given, Captain. I’m simply saving you the bother, as well as saving myself from a final humiliation. If you don’t mind, I’d like to retain a few shreds of dignity.”

He was quite right, she knew, as she rapidly reviewed the appropriate Starfleet protocols in her head, protocols which he knew as well as she did. In that light, his request was perfectly reasonable. Bereft of argument, she did the only thing she could, and turned on her heel to depart. As the door hissed shut, she found herself standing in the corridor, with no idea where to go or what to do. Finally, after several minutes, she made her way slowly to her cabin next door, where she collapsed into the nearest chair.

She sat there for a long time before she gathered herself together enough to return to the bridge and finish her shift.

* * *

By late evening, Kathryn was worn out and sick of the whole sorry mess. She had explained to Tuvok that Chakotay was taking some time off, which covered his absence that day and gave her time to examine her options. Now, after spending hours going over and around the problem, she’d come to the inevitable conclusion that she owed him an apology. Even though captains weren’t ever supposed to be wrong, she realized she’d made a serious error in judgment – she had wronged him severely – and, therefore, it was up to her to make it right.

She debated whether to page him, then decided he might be more willing to listen if she caught him off-guard.

“Computer, locate Comm…Chakotay.”

“Chakotay is in the mess hall.”

Having made her decision to settle their conflict, she wasted no time in heading to deck two. She found Chakotay standing gazing out the viewport, the mess hall dark with the only light coming from the galley. Not wanting to startle him, Kathryn approached carefully, calling his name as she came up beside him.

Unhurriedly, he turned to face her, his expression composed; obviously, he’d been aware of her presence as soon as she came in.

“Chakotay,” she began, “I would like to talk to you, explain why I acted the way I did, and…” she took a deep breath, “offer an apology for the way I treated you. Will you hear me out?”

He gazed down at her steadily, before nodding his head, sighing heavily as he slumped down on the couch behind him. “Explain away, Captain,” he told her. “All I ask is that you be honest this time.”

Kathryn cringed, but bit her tongue, knowing she deserved his rebuke. Carefully, she sat down beside him, folding her hands in her lap as she quickly rehearsed what she had to say.

“When Tuvok first came to me several weeks ago with his suspicions that we had a spy on board, his information was sketchy. He thought he had detected covert transmissions leaving Voyager through the EPS system, but he couldn’t establish a pattern. In vain, he tried every method he could think of, but nothing worked. Mr. Jonas had us completely tangled up in knots.”

Chakotay shrugged. “Seska was a good teacher.”

“Indeed.” Kathryn went on. “Finally, in desperation, we devised a makeshift plan involving Tom Paris.” Glancing down at her hands, she added ruefully. “I realize now that we should have brought you in at that point.”

He snorted softly. “You should have brought me in right at the very beginning. If nothing else, I could have saved you and Tuvok a lot of wasted time.” At her look of surprise, he added, “Neither of you think like a Maquis, so you didn’t have much hope of catching one.”

She bristled a bit at his arrogant assumption, but again held her tongue, not willing to get into an argument over possibilities long past. “I did broach the idea with Tuvok, of including you in on our little plot, but he argued against it, reasoning that given your initial reaction to the idea of Seska being a spy, it would be better not to involve you until we had absolute proof.”

Recalling his thoughts about the quality of his ‘performance’ for Seska, now it was Chakotay’s turn to bristle, but like his captain, he held his peace, letting her finish.

“We were very close to that proof when Neelix began to interfere. I had already decided to brief you fully the next morning, but events got ahead of me.” She paused briefly, before lifting her chin to gaze directly into his eyes. “You’re quite right; you should have been involved right from the start and I’m sorry I didn’t trust my instincts and tell you sooner. I hope you will accept my apology.”

Her words hung in the silence of the room, as Chakotay mulled over what she’d said. He had no doubt of her sincerity now – very rarely did a captain ever apologize for a command decision. As he tried to find an appropriate response that would adequately convey both his residual anger at her betrayal as well as his appreciation for her remorse, he realized that he could do no less than be completely honest with her.

Straightening his back, he returned her direct look. “From the moment we first met, I trusted you, even though at that point, you were my enemy just as much as any Cardassian. Not only did I personally give you my loyalty, I demanded my crew do the same. I thought you trusted me as well.”

His voice intensified. “Three times I’ve been betrayed by the Federation. Once when Starfleet refused to assist my people in their hour of need, once by Tuvok, and now by you.”

Clenching her hands into fists, Kathryn forced her eyes to stay focused on his face as Chakotay’s blunt words landed on her. However, her heart constricted at the anguish evident in his tone. Guilt mixed with pain and regret swept through her, until she couldn’t speak for the lump in her throat. Desperately, she tried to hold onto the tattered remnants of her emotions, but despite her efforts, her eyes filled with tears.

Beside her, his anger dissipating now that he’d finally bared his feelings, Chakotay waited for her response, but she remained silent. After a moment, he leaned forward, his hand gently lifting her chin to see tears sliding slowly down her face.

Staring up at him, her mouth pressed in a tight line, Kathryn made no sound as she sat with her hands gripped tightly together in her lap.

In the half-light, Chakotay wasn’t sure what he was seeing; his hand slid across her cheek, feeling the dampness which he wiped away with gentle fingers. Moving closer, he cupped her face, whispering softly. “Don’t cry.”

On impulse, he bent forward to kiss her very lightly, before wrapping his arms around her and settling against the couch, her head pressed into his neck. He could feel her body tremble and go rigid with tension. Very slowly, he began to stroke her back rhythmically, relaxing the taut muscles until her weight rested solidly against him, and her arms slid around his back.

They remained still for several moments before Kathryn sat up, rubbing her eyes.

“I’m sorry,” she muttered apologetically, “I didn’t mean to cry. I hope you don’t think I’m the sort of woman who uses tears to influence a man.” As she spoke, she looked away, clearly embarrassed at having indulged in such weakness in front of him.

Chakotay smiled at her words, remembering all the times he’d seen her standing on her bridge, feet planted firmly, hands on hips, chin up, her entire posture one of defiance. No, tears were definitely not her style.

She raised a questioning eyebrow at his grin, even as her expression relaxed, realizing the worst was behind them.

Taking her hands, he squeezed them as he replied, still smiling. “I know you’re not, Captain, and I do forgive you for what you did. Maybe this ‘incident’ will help us to understand each other better; I hope so, anyway.”

Returning his smile, she nodded. “I hope so, too. And, in light of our new understanding…would you consider withdrawing your resignation?” Her tone was hopeful, if somewhat hesitant.

Chakotay sat silently as he considered his options, before nodding. Like it or not, they were all in this together. If nothing else, for the good of the crew, he and she had to pull together.

Watching him carefully, Kathryn had a pretty shrewd idea of the thoughts running through his head. Grasping his hands a little tighter, she caught his attention. “Chakotay, I promise I will not shut you out again. From now on, no secrets, no matter what the circumstances.”

At her words, he felt his world right itself and settle back onto an even keel. Breathing a sigh of relief, he stood, pulling her up with him. As he gazed down into her smiling face, he succumbed once more to impulse and bent to kiss her, his mouth moving gently over hers.

Automatically, she began to stiffen before letting herself relax into him and return the kiss. After all, right now, officially he wasn’t her first officer – not yet, anyway.

Lifting his head, he smiled, a hint of mischief in his grin. “Sealed with a kiss,” he told her.

Returning his smile gladly, she nodded and stepped back, her heart full. They would be all right now.

**Author's Note:**

> Originally posted July 13, 2003 - MaryS


End file.
